Protein phylogenetic inference using maximum likelihood with a genetic algorithm.

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H Matsuda

Author Information

H Matsuda: Department of Information and Computer Sciences, Faculty of Engineering Science, Osaka University, Japan.

PMID: 9390255

This paper presents a method to construct phylogenetic trees from amino acid sequences. Our method uses a maximum likelihood approach which gives a confidence score for each possible alternative tree. Based on this approach, we developed a genetic algorithm for exploring the best score tree: randomly generated alternative trees are rearranged so that their scores are improved by utilizing crossover and mutation operators. In a test of our algorithm on a data set of EF-1 alpha sequences, we found that the performance of our algorithm is comparable to that of other tree-construction methods.

Algorithms

Amino Acid Sequence

Animals

Computer Simulation

Databases, Factual

Evolution, Molecular

Models, Genetic

Peptide Elongation Factor 1

Peptide Elongation Factors

Phylogeny

Probability

Proteins

Software

Peptide Elongation Factor 1

Peptide Elongation Factors

Proteins

Journal Article Research Support, Non-U.S. Gov't

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